Not that I have any idea what actually happened but hiring someone at a low level, who seems kind of unreliable, allowing them access to something who's leakage you might not care about, letting everything play out the way it did, seems like something a spy agency would be reasonably adept it.
The women was a contractor, not an agent, so they aren't sacrificing someone they've invested in. etc
So given the choice between "News Site Messed Up Protecting a Source" and "The Whole Thing Was Orchestrated By The Spymasters", you're refusing to make a call because... "who knows?"
I mean, if that's the level of detachment and rationality you're going to apply here... why stop at a mere egg-on-face moment for The Intercept? Surely the NSA could be applying those powers for something more juicy.
The women was a contractor, not an agent, so they aren't sacrificing someone they've invested in. etc
Again, what actually happened, who knows?